Cellular Respiration, Photosynthesis, Cell Communication, and Molecular Genetics

Comprehensive vocabulary flashcards reviewing thermodynamics, enzymes, cellular respiration, photosynthesis, cell communication, DNA replication, and gene expression.

Kinetic energy

The energy of motion, such as moving molecules.

Potential energy

Stored energy, such as energy associated with chemical bonds or a concentration gradient.

Chemical energy

Energy associated with the arrangement of atoms and electrons in molecules.

Exergonic reaction

A chemical reaction that releases free energy, yielding products with less free energy than reactants and a negative change in free energy ($\Delta G$).

Endergonic reaction

A chemical reaction that requires an energy input, yielding products with more free energy than reactants and a positive change in free energy ($\Delta G$).

ATP (adenosine triphosphate)

The cell's energy currency containing three phosphate groups; its hydrolysis to $ADP + P_i$ releases free energy to drive cellular work.

Active site

The specific region of an enzyme where a substrate binds and the chemical reaction occurs.

Activation energy

The energy barrier that must be overcome for a reaction to proceed, which enzymes lower to accelerate reaction rates.

Denaturation

A change in a protein's shape that disrupts its normal biological function.

Competitive inhibitor

An inhibitor molecule that directly competes with the substrate for binding to the active site of an enzyme.

Noncompetitive inhibitor

An inhibitor that binds to an enzyme at a site other than the active site and reduces enzyme activity by altering its function.

Catabolic pathway

A metabolic pathway that breaks down complex molecules and releases free energy overall, such as cellular respiration.

Anabolic pathway

A metabolic pathway that builds larger molecules from smaller components and requires an input of energy overall, such as synthesizing proteins from amino acids.

Oxidation

The loss of electrons from a molecule, atom, or ion during a redox reaction.

Reduction

The gain of electrons by a molecule, atom, or ion during a redox reaction.

Glycolysis

The first stage of cellular respiration in the cytosol that breaks down one $6$-carbon glucose into two $3$-carbon pyruvates without directly requiring oxygen, producing a net yield of $2\,ATP$ and $2\,NADH$.

Substrate-level phosphorylation

A mode of ATP synthesis where an enzyme directly transfers a phosphate group from an organic substrate molecule to ADP.

Pyruvate oxidation

The conversion of two pyruvate molecules into two acetyl-CoA molecules in the mitochondrial matrix, releasing $2\,CO_2$ and producing $2\,NADH$ per glucose.

Citric acid cycle

A cyclic metabolic pathway in the mitochondrial matrix that oxidizes acetyl-CoA, producing $4\,CO_2$, $6\,NADH$, $2\,FADH_2$, and $2\,ATP$ (or equivalent GTP) per original glucose molecule.

Electron transport chain (ETC)

A series of protein complexes in the inner mitochondrial membrane that transfer electrons from NADH and $FADH_2$ to oxygen while pumping protons into the intermembrane space to generate an electrochemical gradient.

Chemiosmosis

The process by which stored potential energy in an electrochemical proton gradient drives the movement of protons down their gradient to power ATP synthesis.

ATP synthase

A membrane-bound protein complex that uses the flow of protons down their gradient across a membrane to synthesize ATP from ADP and inorganic phosphate.

Fermentation

An anaerobic metabolic pathway that does not use an electron transport chain to produce ATP, but instead regenerates $NAD^+$ so glycolysis can continue generating a net of $2\,ATP$ per glucose.

Lactic acid fermentation

A fermentation pathway in which pyruvate accepts electrons from NADH and is reduced to lactate, thereby regenerating $NAD^+$ for glycolysis.

Alcohol fermentation

A fermentation pathway in yeast and certain microorganisms where pyruvate is converted into ethanol and $CO_2$, regenerating $NAD^+$ to sustain glycolysis.

Thylakoid membranes

The internal membrane compartments of chloroplasts where the light reactions of photosynthesis take place.

Stroma

The fluid-filled space surrounding the thylakoid membranes within a chloroplast where the Calvin cycle occurs.

Photosystem II (PSII)

The photosystem acting first in linear electron flow that absorbs light energy and replaces excited electrons by splitting water, releasing $O_2$ and protons ($H^+$).

Photosystem I (PSI)

The photosystem that re-energizes electrons using light energy to facilitate the reduction of $NADP^+$ to NADPH.

Calvin cycle

The light-independent stage of photosynthesis in the stroma consisting of carbon fixation, reduction, and RuBP regeneration phases to incorporate $CO_2$ into organic G3P molecules.

Rubisco

The enzyme in the Calvin cycle responsible for catalyzing the initial fixation of $CO_2$ by attaching it to ribulose bisphosphate (RuBP).

Ligand

A signaling molecule that binds specifically to a receptor protein to initiate a cellular signaling pathway.

Signal transduction

The process by which an extracellular signal is relayed inside the cell through a cascade of proteins or second messengers to produce a cellular response.

Protein kinase

An enzyme that transfers a phosphate group from ATP to a protein (phosphorylation), typically modifying its activity.

Protein phosphatase

An enzyme that removes phosphate groups from proteins (dephosphorylation), often deactivating signaling pathways.

Second messenger

A small, non-protein molecule or ion, such as cAMP or $Ca^{2+}$, that relays and amplifies signals inside the cell.

G protein-coupled receptors (GPCRs)

A family of cell-surface transmembrane receptors that interact with G proteins upon ligand binding to regulate downstream targets.

Receptor tyrosine kinases (RTKs)

Cell-surface receptors that dimerize upon ligand binding and phosphorylate tyrosine residues, recruiting and activating downstream signaling proteins.

Ligand-gated ion channel

A membrane receptor that opens or closes its channel pore in response to ligand binding, altering the flow of ions across the plasma membrane.

Intracellular receptor

A receptor protein located inside the cytoplasm or nucleus that binds small, nonpolar signaling molecules (such as steroid hormones) that diffuse across the plasma membrane.

Semiconservative replication

The model of DNA replication in which each newly formed double helix contains one intact parental strand and one newly synthesized daughter strand.

Helicase

The enzyme that unwinds and separates the two complementary strands of parental DNA ahead of the replication fork.

Topoisomerase

An enzyme that relieves the torsional twisting strain and supercoiling ahead of the replicating DNA fork.

Primase

An enzyme that synthesizes short RNA primers to provide the free 3'-OH group needed for DNA polymerase to initiate synthesis.

DNA polymerase

An enzyme that adds complementary DNA nucleotides to a growing strand exclusively in the $5' \rightarrow 3'$ direction and proofreads for replication errors.

DNA ligase

An enzyme that seals nicks in the sugar-phosphate backbone by joining adjacent DNA fragments, such as Okazaki fragments on the lagging strand.

Okazaki fragments

Short, discontinuously synthesized segments of DNA produced on the lagging strand moving away from the replication fork.

Telomeres

Repetitive, non-coding nucleotide sequences at the ends of eukaryotic chromosomes that protect vital genetic information from degradation.

Central dogma

The fundamental concept describing the flow of genetic information from DNA to RNA to protein ($\text{DNA} \rightarrow \text{RNA} \rightarrow \text{protein}$).

Transcription

The process in which RNA polymerase synthesizes a complementary, antiparallel RNA molecule in the $5' \rightarrow 3'$ direction using a DNA template strand.

Alternative splicing

A eukaryotic RNA processing mechanism where introns are removed and different combinations of exons are joined to yield distinct mature mRNA transcripts from a single gene.

Codon

A sequence of three consecutive nucleotides in mRNA that specifies a particular amino acid or a termination signal during translation.

Transfer RNA (tRNA)

An adaptor RNA molecule that carries a specific amino acid to the ribosome and contains an anticodon complementary to an mRNA codon.